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accession-icon SRP128490
RNA sequencing to study transcriptomic changes in DLD-1 (colorectal adenocarcinoma) cells exposed to soft polyacrylamide matrices (~2 kPa and ~55 kPa) for short time scale of 90 minutes
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

Aim: To examine transcriptional changes in DLD-1 cells exposed to softer matrices (2 kPa and 55 kPa) and identify the chromosomes that are enriched with maximmally deregulated genes Methods: DLD-1 cells (otherwise growing on stiff tissue culture plastic substrates) were exposed to softer matrices for 90 minutes and to collagen coated glass coverslips (served as control) served as control) Results: RNA sequencing revealed nearly equivalent transcriptional deregulation in cells on both the polyacrylamide matrices (783 genes up and 872 genes down on 2 kPa, 649 genes up and 783 genes down on 55 kPa) when compared to cells on glass. Additionally, GO classification revealed that unique sets of transcriptionally deregulated genes (log fold=2) belonged to pathways associated with transcription regulation, chromatin organization, cell cycle and DNA damage/repair Results: We identified chromosomes 1, 2, 3, 6, 7, 10, 12, 14, 17 and 19 to be maximally enriched with the deregulated genes on softer matrices (log fold=2), while chromosomes 13, 18 and 21 showed minimal enrichment of deregulated genes. We also examined the spatial organization of chromosome 1, 18 and 19 territories in cells on softer matrices (using 3D-FISH) and observed that these chromosomes were mislocalized away from their conserved nuclear locations Conclusions: Our study reports the transcriptomic changes in DLD-1 cells upon lowering of extracellular substrate stiffnes and its impact on the spatial positioning of chromosome territories Overall design: RNA Seq profiles for DLD-1 cells on soft polyacrylamide matrices of ~2 kPa and ~55 kPa (reference - glass) were generated across 2 independent biological replicates using Illumina HiSeq platform

Publication Title

Emerin modulates spatial organization of chromosome territories in cells on softer matrices.

Sample Metadata Fields

Cell line, Subject

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accession-icon GSE10184
2 or 3 Day Post Amputation Vehicle or TCDD Exposed
  • organism-icon Danio rerio
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Zebrafish Genome Array (zebrafish)

Description

Exposures to dioxin, including 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) cause a wide array of toxicities in vertebrates and is mostly considered to be mediated through the inappropriate activation of the aryl hydrocarbon receptor (Ahr) signaling pathway. Although transcriptional regulation by Ahr is widely studied, the molecular mechanisms responsible for the adverse outcomes after Ahr activation are largely unknown. To identify the important events downstream of AHR activation that play an actual role in the toxic responses, we employed the zebrafish caudal fin regeneration models since Ahr activation blocks the regenerative process. Zebrafish regenerate their caudal fins by an orchestrated progression of cell migration, differentiation and proliferation controlled by a multitude of signaling pathways. This complex process was exploited as an in vivo platform to identify cross talk between Ahr and other signaling pathways. Global genomic analysis was performed in the larval regenerating fin tissue after exposure to TCDD in order to identify genes differentially regulated after Ahr activation. Comparative toxicogenomic analysis revealed that both adult and larval fins respond to TCDD during regeneration with mis-expression of Wnt signaling pathway members and Wnt target genes.

Publication Title

Crosstalk between AHR and Wnt signaling through R-Spondin1 impairs tissue regeneration in zebrafish.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP009134
sRNA profiles of control adults, postdauer adults, larva L3, and dauer stages of C. elegans
  • organism-icon Caenorhabditis elegans
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer II

Description

Early environmental experiences and life histories profoundly influence adult phenotypes via as yet poorly understood mechanisms. We previously showed that wild-type adult C. elegans that transiently passed through the stress-induced dauer larval stage (post-dauers) exhibit different gene expression patterns, genome-wide chromatin structure, and life history traits when compared to adults that bypassed the dauer stage (controls). Here we show that endogenous small inhibitory RNAs (endo-siRNAs) and siRNA pathways may mediate developmental history-dependent phenotypic diversity. Deep sequencing of small RNA libraries show changes in endo-siRNA levels in post-dauer as compared to control animals, and meta analyses indicate that specific endo-siRNA pathways are targets of developmental history-dependent reprogramming. We demonstrate that mutations in specific endo-siRNA pathways affect the expected gene expression and chromatin state changes in post-dauer animals, and also disrupt their increased brood size phenotype. We find that the chromatin state and endo-siRNA distribution in dauers is also distinct and suggest that this remodeling in dauers provides a template for the subsequent establishment of adult post-dauer profiles. Together, our results imply a critical mechanistic role for endo-siRNA pathways in mediating early experience-dependent phenotypic divergence in adults, and suggest that regulation of these pathways contribute to increased fitness via non-genetic mechanisms. Overall design: We deep-sequenced small RNA libraries from 2 biological replicates each of control and postdauer adults, and one biological each of larval L3 and dauer stages.

Publication Title

Developmental programming modulates olfactory behavior in C. elegans via endogenous RNAi pathways.

Sample Metadata Fields

Cell line, Subject

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accession-icon GSE10188
Comparative genomic analysis between adult and larval fin regeneration
  • organism-icon Danio rerio
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Zebrafish Genome Array (zebrafish)

Description

Zebrafish have the remarkable ability to regenerate body parts including the heart, spinal cord and fins by a process referred to as epimorphic regeneration. Recent studies have illustrated that similar to adult zebrafish, early life stage-larvae also possess the ability to regenerate the caudal fin. A comparative genomic analysis was used to determine the degree of conservation in gene expression among the regenerating adult caudal fin, adult heart and larval fin. Results indicate that these tissues respond to amputation/injury with strikingly similar genomic responses. Comparative analysis revealed raldh2, a rate-limiting enzyme for the synthesis of Retinoic acid (RA), as one of the highly induced genes across the three regeneration platforms.

Publication Title

Comparative expression profiling reveals an essential role for raldh2 in epimorphic regeneration.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE103974
Gene expression profiling of thymus samples from myasthenia gravis patients.
  • organism-icon Homo sapiens
  • sample-icon 13 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

Autoimmune myasthenia gravis (MG) is characterized by thymic abnormalities such as hyperplasia and thymoma. Thymus plays an important role in self-tolerance and is involved in initiation and progression of the disease.

Publication Title

MicroRNA and mRNA expression associated with ectopic germinal centers in thymus of myasthenia gravis.

Sample Metadata Fields

Specimen part, Disease stage

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accession-icon GSE21467
Loss of Caenorhabditis elegans UNG-1 uracil-DNA glycosylase affects apoptosis in response to DNA damaging agents.
  • organism-icon Caenorhabditis elegans
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix C. elegans Genome Array (celegans)

Description

The nematode Caenorhabditis elegans has been used extensively to study responses to DNA damage. In contrast, little is known about DNA repair in this organism. C. elegans is unusual in that it encodes few DNA glycosylases and the uracil-DNA glycosylase (UDG) encoded by the ung-1 gene is the only known UDG. C. elegans could therefore become a valuable model organism for studies of the genetic interaction networks involving base excision repair (BER). As a first step towards characterization of BER in C. elegans, we show that the UNG-1 protein is an active uracil-DNA glycosylase. We demonstrate that an ung-1 mutant has reduced ability to repair uracil-containing DNA but that an alternative Ugi-inhibited activity is present in ung-1 nuclear extracts. Finally, we demonstrate that ung-1 mutants show altered levels of apoptotic cell corpses formed in response to DNA damaging agents. Increased apoptosis in the ung-1 mutant in response to ionizing radiation (IR) suggests that UNG-1 contributes to repair of IR-induced DNA base damage in vivo. Following treatment with paraquat however, the apoptotic corpse-formation was reduced. Gene expression profiling suggests that this phenotype is a consequence of compensatory transcriptomic shifts that modulate oxidative stress responses in the mutant and not an effect of reduced DNA damage signaling.

Publication Title

Loss of Caenorhabditis elegans UNG-1 uracil-DNA glycosylase affects apoptosis in response to DNA damaging agents.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE23528
Light/dark- and temperature-regulated transcriptional rhythms in adult Caenorhabditis elegans
  • organism-icon Caenorhabditis elegans
  • sample-icon 95 Downloadable Samples
  • Technology Badge Icon Affymetrix C. elegans Genome Array (celegans)

Description

Most organisms have an endogenous circadian clock that is synchronized to environmental signals such as light and temperature. Although circadian rhythms have been described in the nematode C. elegans at the behavioral level, these rhythms appear to be relatively non-robust. Moreover, in contrast to other animal models, no circadian transcriptional rhythms have been identified. Thus, whether this simple nematode contains a bona fide circadian clock remains an open question.

Publication Title

Genome-wide analysis of light- and temperature-entrained circadian transcripts in Caenorhabditis elegans.

Sample Metadata Fields

Specimen part, Time

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accession-icon SRP150459
Transcriptional profiling by 4SU-seq in mouse ESCs and ESC-derived neural progenitor cells.
  • organism-icon Mus musculus
  • sample-icon 31 Downloadable Samples
  • Technology Badge IconNextSeq 550

Description

Nascent RNA was metabolically labelled with 4SU in undifferentiated and ESC-derived neural progenitor cells (NPCs). 4SU incorporated RNA was isolated and deep-sequenced at day 0 (ESCs), 3, 5 and 7 of differentiation. NPC differentiation was monitored through expression of a GFP reporter insereted into the Sox1 locus (46C reporter ESC line; PMID: 12524553). The aim was to monitor changes in transcription as ESCs differentiate into NPCs and relate this to enhancer activity. Overall design: For each of the 4 differentiation time points, two independent biological replicates were prepared and sequenced. For each assayed time point, both merged and individual replicate 4SU-seq profiles were generated.

Publication Title

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE55486
Defective Mitophagy in XPA via PARP1 activation and NAD+/SIRT1-depletion: Implications for neurodegeneration
  • organism-icon Mus musculus, Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip, Illumina MouseRef-8 v2.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Defective mitophagy in XPA via PARP-1 hyperactivation and NAD(+)/SIRT1 reduction.

Sample Metadata Fields

Sex, Cell line, Treatment

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accession-icon GSE15610
Knockout of the selenocysteine tRNA (Trsp) gene in mouse macrophage
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Comparative analysis of gene expression in bone marrow-derived macrophages (BMDM) from trsp knockout mice (Trspfl/fl-LysM-Cre+/-) and Control (Trspfl/fl-LysM-Cre-/-) mice.

Publication Title

Selenoproteins regulate macrophage invasiveness and extracellular matrix-related gene expression.

Sample Metadata Fields

Sex, Treatment

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refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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